The sub box will flex and vibrate and can cause your amps internals to vibrate as well. You can wreck amp this way (from what I have heard) but I have never done it personally, I just use the back of a seat or ground.
for once i totally agree with MS,WOOO, ive had a bad experience with an amp being on top of the sub box and it rattled my amp right out of commision but it took a lil while for it too happen but none the less it happened. usually the best spots are the left rear or right rear of the trunk if possible or right behind the rear seats.